Personally, I've never tried to purchase 500's at the gate, but FT conventional wisdom has it that the GA's don't have the time (or aren't willing to spend it) to process payments for 500's at the gate. Every account I've read has indicated that the GA's basically say you have to have the certs already in your account or you can't get the upgrade. Some FT'ers have suggested that you can purchase them by phone before claiming your upgraded seat, but I don't know what the success rate is with that approach.

As for the boarding pass question, if your IAD-SFO upgrade has cleared by the time you check in at BDL, it's a no brainer: you purchase the 500's at that time and get your BP for your upgraded seat. However, if your IAD-SFO upgrade hasn't cleared by that time, you'll get the BP for your regular E+ seat, along with a Departure Management (DM) card for the waitlisted upgrade.

The problem is that IME, if they upgrade you, they give away your seat to someone else before you confirm & provide the 500's for your upgraded seat. That means that if you decline the upgrade, they've already put someone else in your seat and the fact that you hold a (now obsolete) BP for that seat won't matter. They'll still put you in whatever seat is available and give you a new BP.

As a side note, it works this way for OpUp's, too. Several times, I've been on a different PNR from Mrs. hockeyguy and they've OpUp'd me without her. By the time I've declined my single upgraded seat, they've already put someone else in my original seat next to my wife which has made it very complicated to get us reseated together again, parciularly if we want to keep the good seats we originally selected and not get sent back to E-. As a result, we always try to travel on the same PNR now.